Calhoun's proposal to Shelby after he comes back in Excalibur: Restoration is definitely one.
Burgoyne following Selar to Vulcan for Xyon and their relationship. That whole storyline is one giant scoop of heartwarming.
Out-of-universe, the series appeared to end on a Downer Ending with Blind Man's Bluff thanks to Peter David's stroke which prevented him from potentially ever writing again. Then, thank the Great Bird of the Galaxy, he made a significant recovery and was so enamored with the series he wrote three more volumes.